Sequence specificity of 125I-labelled Hoechst 33258 in intact human cells

In silico investigation of DNA minor groove binding bibenzimidazoles in the context of UVA phototherapy

The versatility of DNA minor groove binding bibenzimidazoles extends to applications in cancer therapy, beyond their typical use as DNA stains. In the context of UV_A phototherapy, a series of halogenated analogues designated ortho-, meta-, and para-iodoHoechst have been investigated. Phototoxicity involves dehalogenation of the ligands following exposure to UV_A light, resulting in the formation of a carbon-centred radical. While the cytotoxic mechanisms have been well established, the nature and severity of DNA damage induced by the ortho-, meta-, and para-iodoHoechst isomers requires clarification. Our aims were to measure and compare the binding constants of iodoHoechst analogues, and to determine the proximity of the carbon-centred radicals formed following photodehalogenation to the C1', C4', and C5' DNA carbons. We performed molecular docking studies, as well as classical molecular dynamics simulations to investigate the interactions of Hoechst ligands with DNA including a well-defined B-DNA dodecamer containing the high affinity AATT minor groove binding site. Docking highlighted the binding of Hoechst analogues to AATT regions in oligonucleotides, nucleosomes, and origami DNA helical bundles. Further, MD simulations demonstrated the stability of Hoechst ligands in the AATT-containing minor groove over microsecond trajectories. Our findings reiterate that the efficiency of dehalogenation per se, rather than the proximity of the carbon-centred radicals to the DNA backbone, is responsible for the extreme phototoxicity of the ortho- isomer compared to the meta- and para-iodoHoechst isomers. More generally, our analyses are in line with the potential utility of ortho-iodoHoechst in DNA-targeted phototherapy, particularly if combined with a cell-specific delivery system.

Molecular Dynamics Simulations of Dna and Its Complexes

This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA–ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands—including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.

Minor groove binding of the food colorant carmoisine to DNA: spectroscopic and calorimetric characterization studies

The interaction of the food additive carmoisine with herring testes DNA was studied by multifaceted biophysical techniques. Carmoisine exhibited hypochromic effects in absorbance, whereas in fluorescence the intensity enhanced upon complexation with DNA. Energy transfer from the DNA base pairs to carmoisine molecules occurred upon complexation. A groove binding model of interaction was envisaged for carmoisine-DNA complexation from 4',6-diamidino-2-phenylindole (DAPI) and Hoechst displacement studies. The binding of carmoisine stabilized the DNA structure against thermal denaturation. The binding induced moderate conformational perturbations in the B-form structure of DNA. The binding affinity (10(4) M(-1)) values, calculated from absorbance and fluorescence data, and calorimetry titrations were in close agreement with each other. The binding was characterized to be exothermic and favored by small negative enthalpic and large positive entropic contributions. Salt-dependent calorimetric studies revealed that the binding reaction was dominated by nonpolyelectrolytic forces. The negative heat capacity value suggested the role of hydrophobic effect in the interaction.

DNA Ligands as Radioprotectors: Molecular Studies with Hoechst 33342 and Hoechst 33258

Following earlier reports of radioprotection of cells by Hoechst 33342, we have investigated radioprotection of isolated DNA by the minor groove binders Hoechst 33258 and Hoechst 33342. Analysis of radiation-induced single strand breakage in plasmid DNA (pBR322) showed concentration-dependant protection, up to a dose-modifying factor of 9.3 for 25 microM Hoechst 33258, at which the ligand: bp ratio was 0.67. Since the ligands bind at discrete sites along DNA, sequencing gel analysis was used to investigate the radioprotective effects of the ligands both at and between the ligand-binding sites. These experiments showed that although protection was more pronounced at the binding sites, there was also some reduction in strand-breakage between binding sites. Detailed analysis at a particular site, the EcoR1 site in a 3'-32P-endlabelled 100bp restriction fragment from pBR322, showed that protection was most pronounced at the 'inner T': GAATTC. Irradiation of a synthetic oligodeoxynucleotide containing a single ligand-binding site, and labelled at the 5'-end, gave the expected doublet bands in high resolution gels, corresponding to fragments with 3'-phosphoryl- and 3'-phosphorylglycollate terminii. In the Hoechst 33258-protected sample, the 3'-phosphorylglycollate band was preferentially suppressed within the binding site. These results, together with published crystal structure data for a Hoechst 33258/dodecamer complex, suggest that the site-specific radioprotection may be due to H-atom donation from the benzimidazole NH groups in the ligand to radiation-induced radicals on 4'-deoxyribosyl carbons. In contrast to the experiments with purified DNA, in which the two ligands yielded similar results, Hoechst 33342 was a much more active radioprotector in experiments with intact cells. For 20 microM Hoechst 33342, the dose-modifying factor was 1.7 at 1% survival and 1.3 at 10% survival, whereas the same level of Hoechst 33258 yielded barely detectable protection, perhaps due to a demonstrably lower cellular uptake. Presumably the radioprotection of cells by Hoechst 33342 is due to suppression of DNA strand breakage, and further investigation of the protection mechanism(s) should enable development of improved radioprotectors.

Kinetics of Micronucleus Induction by125I-labelled Thyroid Hormone in Hormone-responsive Cells

Two cell lines, CHO and GC, different in their tissue origin, were investigated with the aim of discovering the correlation between the level of 125I-T3 binding and chromosomal damage induced by 125I decay. Incubation of cells with 125I-T3 has been performed in two exposure schedules: continuous incubation for one to six cell cycles and a pulse-chase schedule involving exposure for one cell cycle. The cellular uptake of 125I-T3, its compartmentization and kinetics were different in the two cell lines. GC cells contained about 7 times more 125I-T3 than CHO cells when incubated with the same external 125I activity concentration (74 kBq of 125I-T3 ml-1 medium). Approximately 70% of the cellular 125I-T3 was found in nuclei of GC cells and only 5% in the nuclei of CHO cells. During the long-term incubation of GC cells with 74 kBq of 125I-T3 ml-1 medium, the 125I activity concentration in cells and their nuclei initially decreased by a half, and thereafter reached a plateau after the third doubling time. In CHO cells and nuclei a very slow linear increase of 125I activity was observed. In GC cells, micronucleus frequency was found to be correlated with nuclear 125I activity. One cell cycle pulse labelling with 74 kBq of 125I-T3 ml-1 medium caused a significant enhancement of micronucleus frequency above the control level during six doubling times, with a maximum at the first post-labelling doubling time. In GC cells continuously incubated with 74 kBq of 125I-T3 ml-1 medium, the micronucleus frequency increased with the incubation time. A model of T3 receptor-dependent dose delivery to nuclei of GC cells continuously incubated with 125I-T3 is proposed. The frequency of micronuclei in the CHO cell line continuously incubated with 125I-T3 did not differ significantly from the control, whereas in the pulse-chase schedule the mean frequency of micronucleated binuclear cells was lower during 4 post-labelling doubling times (significantly at the first and second post-labelling doubling time and insignificantly at the later doubling times) than in the control. Incubation of GC cells with various activity concentrations in medium for four cell cycles resulted in a linear increase of 125I activity in cells and nuclei; however, with a saturation in the region of highest 125I-T3 concentrations used. The frequency of binuclear cells bearing micronuclei was linearly dependent on the nuclear 125I-T3 concentration.

Plasmid breakage by (125)I-labelled DNA ligands: effect of DNA-iodine atom distance on breakage efficiency

PURPOSE

The aim of the study is to establish the relationship between the efficiency of DNA double-stranded breakage by (125)I-labelled DNA ligands and the distance from the decaying atom to the helical axis.

MATERIALS AND METHODS

Two new iodinated minor groove binding ligands were synthesized which, on the basis of molecular modelling studies, place the iodine atom at different distances from the DNA helical axis (namely 7.4 and 11.2 A degrees ). Plasmid DNA breakage experiments, in both buffer-only and buffer + 2M dimethylsulfoxide (DMSO), were used to determine the efficiency of induction of internal double-stranded breaks (DSB) of the two new ligands, as well as that for (125)I-Hoechst 33258, which is characterized by a helical axis-iodine atom distance of 9.1 A degrees .

RESULTS

The results showed a progressive decrease in the efficiency of DNA DSB induction with the axis-iodine atom distance, for both incubation conditions. The distance-damage relationship was somewhat steeper than previously predicted from the theoretical studies by Humm and Charlton, based on radical-mediated damage. Another distinctive trend was revealed by comparison of breakage efficiency with and without DMSO. The extent of DMSO protection increased significantly with DNA-iodine distance.

CONCLUSIONS

The steeper than predicted decrease in DSB induction with DNA-iodine distance is consistent with a substantial contribution to DNA breakage of the charge neutralization effect (arising from the transient positive charge left on the daughter Te atom), and the expectation that this contribution would be very dependent on the distance of the site of hole injection from the base-pair pi-stack. An important caveat to the results and conclusions is the need to confirm the estimated helical axis-iodine distances with X-ray crystallography studies, and for further exemplification with a more extensive collection of DNA ligands.

Using Hoechst 33342 to target radioactivity to the cell nucleus

We have explored the use of Hoechst 33342 (H33342) to carry radioactivity to the cell nucleus. H33342 enters cells and targets DNA at adenine-thymine-rich regions of the minor groove. Considerable membrane blebbing and ruffling occur in CHO cells within minutes after its addition to the culture medium in micromolar quantities. Blue vesicles are apparent in the cell cytoplasm, and by 30 min the nuclei are stained dark blue. Upon its binding to DNA, a visible emission shift of the dye can be observed with fluorescence microscopy. We have radioiodinated (125I) H33342 and specifically irradiated nuclear DNA by incubating CHO cells with 125I-H33342 at 37 degrees C and accumulating 125I decays at -90 degrees C. At various times, the cells are thawed and assayed for survival (clonogenicity) and DSB (gamma-H2AX) formation. 125I-H33342 decay leads to a monoexponential decrease in cell survival with a D0 of 122 125I decays per cell and a linear increase in DNA DSB induction (equivalent to 15 gamma-H2AX foci/cell). Cell death is not modified by the radioprotective effects of H33342 because we use considerably lower concentrations than those that provide a slight protection against gamma radiation. We conclude that cell killing by 125I-H33342 and the induction of gamma-H2AX foci are highly correlated.

DNA Breakage by Decay of Auger Electron Emitters: Experiments with123I-iodoHoechst 33258 and Plasmid DNA

The Auger electron-emitting isotope 123I is of interest in the context of potential exploitation of Auger electron emitters in radioimmunotherapy. The efficiency of induction of cytotoxic lesions by decay of DNA-associated 125I, the prototype Auger electron emitter, is well established, but its long half-life (60 days) is a limitation. However, the advantage of the much shorter half-life of 123I (13.2 h) might be outweighed by its "weaker" Auger electron cascade with an average of 8-11 Auger electrons, compared to about 15-21 electrons for 125I. Accordingly, the efficiency of DNA breakage for DNA-associated 123I was investigated by incubation of 123I-iodoHoechst 33258 with plasmid DNA. The efficiency of double-strand break induction by decay of 123I was 0.62 compared to 0.82 per decay of 125I in the same experimental system. In the presence of dimethylsulfoxide, the values were 0.54 and 0.65 for decay of 123I and 125I, respectively. The results also showed that at a very low ligand/plasmid molar ratio (<1), the majority of cleavage seemed to occur at a particular site on the plasmid molecule, indicating preferential binding of the 123I-ligand to a unique site or a cluster of neighboring sites.

Plasmid DNA breakage by decay of DNA-associated auger emitters: experiments with 123I/125I-iodoHoechst 33258

PURPOSE

The Auger emitting isotope 123I has a much shorter half-life (13.2 hours), than 125I, the prototype Auger emitter. Monte Carlo simulations and cell culture studies indicate that decay of 123I covalently incorporated into DNA is about half as effective as 125I in terms of DNA breakage and cytotoxicity. The aim of the present study is to assess the DNA breakage efficacy of 123I that is non-covalently associated with DNA, using the minor groove binding ligand iodoHoechst 33258.

MATERIALS AND METHODS

Plasmid (pBR322) DNA was incubated with mixtures of [123I]- and [125I]-iodoHoechst 33258, and DNA double strand breakage (DSB) assessed by assaying the relative amounts of intact, relaxed and linear plasmid forms separated by agarose gel electrophoresis. This "double-label" approach provides a measure of the ratio of probabilities of DSB formation per decay for these two isotopes, with much higher precision than comparing the absolute probabilities for the individual isotopes, principally because it avoids the requirement to accurately determine the fraction of bound ligand.

RESULTS

Our results indicate that the ratio of DSB probability per decay of 123I to that of 125I is 0.63 +/- 0.03. The ratio does not change much with addition of dimethyl sulfoxide (DMSO) to the incubation mixture--0.65 +/- 0.03. This ratio agrees well with the relative efficiency of the two isotopes reported in theoretical and experimental studies, using various endpoints.

CONCLUSIONS

In considering the possible exploitation of the Auger effect in cancer therapy, the modest decrease in DNA breakage efficacy for 123I compared to 125I might be more than compensated for by the advantage of the much shorter half-life. The 60-day half-life of 125I imposes severe limitations in terms of radiation protection.

Allometry of base pair specific-DNA contents in Tetrapoda

Cells of 82 species of Tetrapoda were stained with DNA base pair specific fluorochromes (Hoechst 33258 and olivomycin) and studied by means of flow cytometry. The genome size range was about 50-fold. The class Amphibia, which had the widest range of genome size variation (about 20-fold), exhibited linear allometry in their base pair specific DNA contents (bps-C-values), i.e., the more DNA they had, the lower the quotient of AT-pairs (C(AT) = 0.13 + 0.87 x C(GC), r = +0.998). Data for Mammalia, pooled with amphibians, fell on the same allometric line at the lower extreme end of genome size range, supporting the correlation. Reptilia-Aves (or Reptilia alone) pooled with Amphibia did not conform with this relationship. Reptilia-Aves form their own line (zone); pooled with Mammalia, this group showed no regularities in the relationship of their bps-DNA contents. Besides revealing the allometry of bps-C-values, these data indicate an integral genomic feature, localization within the same regression line, which Mammalia share with Amphibia but not with recent Reptilia (and Aves). These data also suggest that the relationship between DNA base frequencies and genome size is nonlinear (reciprocal); to obtain a linear relationship, the bps-C-values should be used. It is also concluded that caution is needed when DNA-content is measured for comparative purposes using a fluorescent dye which is known to be base-pair specific. DNA content values obtained with fluorochromes with different specificity may differ as much as by a factor of 1.8, the average discrepancy level is about 14%.

A survey of the sequence-specific interaction of damaging agents with DNA: emphasis on antitumor agents

This article reviews the literature concerning the sequence specificity of DNA-damaging agents. DNA-damaging agents are widely used in cancer chemotherapy. It is important to understand fully the determinants of DNA sequence specificity so that more effective DNA-damaging agents can be developed as antitumor drugs. There are five main methods of DNA sequence specificity analysis: cleavage of end-labeled fragments, linear amplification with Taq DNA polymerase, ligation-mediated polymerase chain reaction (PCR), single-strand ligation PCR, and footprinting. The DNA sequence specificity in purified DNA and in intact mammalian cells is reviewed for several classes of DNA-damaging agent. These include agents that form covalent adducts with DNA, free radical generators, topoisomerase inhibitors, intercalators and minor groove binders, enzymes, and electromagnetic radiation. The main sites of adduct formation are at the N-7 of guanine in the major groove of DNA and the N-3 of adenine in the minor groove, whereas free radical generators abstract hydrogen from the deoxyribose sugar and topoisomerase inhibitors cause enzyme-DNA cross-links to form. Several issues involved in the determination of the DNA sequence specificity are discussed. The future directions of the field, with respect to cancer chemotherapy, are also examined.

Synthetic DNA minor groove-binding drugs

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

Enhanced DNA alkylation activities of Hoechst 33258 analogues designed for bioreductive activation

A series of analogues of Hoechst 33258, designed to be subject to bioreductive activation, were synthesized, and interactions between these compounds and pBR322 DNA were investigated. Compounds containing a quinone group reacted with DNA via two possible pathways in the presence of reductants NADH or NADPH: radical cleavage and DNA alkylation. The corresponding dimethoxy compounds, which are not subject to reduction, showed very weak DNA binding ability. The strength of alkylation reaction of the quinone derivatives is related to leaving group ability. Furthermore, the quinone compounds preferentially alkylate DNA at 5'-CG and TG sequences rather than at the AT sites preferred as binding sites of Hoechst 33258.

DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258

The complexes of Hoechst 33258 with poly[d(A-T)2], poly[d(I-C)2], and poly[d(G-C)2], and poly[d(G-m5C)2] were studied using linear dichroism, CD, and fluorescence spectroscopies. The Hoechst-poly[d(I-C)2] complex, in which there is no guanine amino group protruding in the minor groove, exhibits spectroscopic properties that are very similar to those of the Hoechst-poly[d(A-T)2] complex. When bound to both of these polynucleotides, Hoechst exhibits an average orientation angle of near 45 degrees relative to the DNA helix axis for the long-axis polarized low-energy transition, a relatively strong positive induced CD, and a strong increase in fluorescence intensity--leading us to conclude that this molecule also binds in the minor groove of poly[d(I-C)2]. By contrast, when bound to poly[d(G-C)2] and poly[d(G-m5C)2], Hoechst shows a distinctively different behavior. The strongly negative reduced linear dichroism in the ligand absorption region is consistent with a model in which part of the Hoechst chromophore is intercalculated between DNA bases. From the low drug:base ratio onset of excitonic effects in the CD and fluorescence emission spectra, it is inferred that another part of the Hoechst molecule may sit in the major groove of poly[d(G-C)2] and poly[d(G-m5C)2] and preferentially stacks into dimers, though this tendency is strongly reduced for the latter polynucleotide. Based on these results, the importance of the interactions of Hoechst with the exocyclic amino group of guanine and the methyl group of cytosine in determining the binding modes are discussed.

DNA damage induction by 125I-estrogen

DNA damage induced by the radioactive decay of 125I-estrogen (125I-VME2) in an estrogen receptor expressing CHO cell line, CHO-ER, was measured. 125I-VME2 targeted 125I atoms proximal to DNA estrogen response elements (EREs). 125I decays were accumulated at -135 degrees C, and thereafter assayed by alkaline and neutral filter elution techniques to measure DNA single strand break (ssb) and double strand break (dsb) induction respectively. Increasing DNA damage (both ssbs and dsbs) was detected after exposure of cells to increasing concentrations of 125I-VME2. DNA ssb and dsb dose-response curves for 125I-VME2 were multiphasic. The rates of DNA damage induction by the decay of 125I-VME2 was determined by comparing slopes of all data or by comparing initial slopes. DNA ssb induction per 125I-VME2 decay was approximately 2 times greater compared with DNA dsb induction. 125I-VME2 decay induced approximately 4-8 times more DNA dsbs than 125IUdR decay.

Cellular and subcellular studies of the radiation effects of Auger electron-emitting estrogens

We studied the effect of 123I-labeled estrogen (123I-E) in estrogen receptor (ER)-rich cells in culture and in cell free model systems in vitro to elucidate the nature of the radiotoxicity for ER + cells of estrogens containing nuclides which emit Auger electrons. In cells the 123I-E caused a dose-dependent, unlabeled estrogen-inhibitable induction of chromosome aberrations. A dose of about 1000 decays per cell, which is approximately the mean lethal dose for these cells, resulted in an average of 1 chromosome break per cell. This supports the hypothesis that the lethal lesion induced by 123I-E is a chromosome break. Incubation of 123I-E/ER complex, but not 123I-E alone, with 27-mer duplex estrogen response element (ERE) DNA produced a dose-dependent cleavage of the ERE. However, we were unable to detect any fragmentation of either the 66 kDa full length ER in cell extracts or a purified 31 kDa hormone binding domain when incubated with excess 123I-E. Thus it appears that 123I-E effects its radiotoxicity by binding to ER, associating with ERE DNA and, by directing high LET radiation to DNA, inducing lethal chromosome breaks.

The interaction of hedamycin and DC92-B in a sequence selective manner with DNA in intact human cells

The sequence specificity of the pluramycin antibiotics hedamycin and DC92-B, was established in intact human cells using a linear amplification system. In this system an oligonucleotide primer is extended by Taq DNA polymerase up to a damage site. The products are run on a DNA sequencing gel and the damage can be determined to the exact base pair. The human repetitive alpha RI DNA was used as the target DNA sequence for these experiments. It was found that G residues were the main site of adduct formation, for both hedamycin and DC92-B. The sequences 5'-TGT and 5'-CGT were the most intense sites of DNA damage. A comparison of the DNA damage intensity in intact cells and purified DNA revealed that the sequence position of adduct formation was very similar in the two environments. However, a densitometric comparison of the damage intensity in the two environments revealed significant differences. Two regions were found (120 and 130 bp in length) where the damage intensity was relatively lower in intact cells compared to purified DNA. But at the boundaries of these sequences, there were regions (approx. 50-60 bp long) that were relatively more damaged in intact cells compared to purified DNA. One explanation of this phenomenon is the presence of a protecting nucleosome core on each of the 120/130 bp regions and flanking nucleosome linker regions of 50-60 bp. This postulated sequence phasing of the nucleosomes corresponds almost exactly with the major nucleosome phasing found in African green monkey cells. Also the centromere protein B binding site is found in the border region between the nucleosome core and linker DNA regions. Hedamycin and DC92-B produced nearly identical results in this human cell system.

Sequence-specific DNA double-strand breaks induced by triplex forming 125I labeled oligonucleotides

A triplex-forming oligonucleotide (TFO) complementary to the polypurine-polypyrimidine region of the nef gene of the Human Immunodeficiency Virus (HIV) was labeled with 125I at the C5 position of a single deoxycytosine residue. Labeled TFO was incubated with a plasmid containing a fragment of the nef gene. Decay of 125I was found to cause double-strand breaks (DSB) within the nef gene upon triplex formation in a sequence specific manner. No DSB were detected after incubation at ionic conditions preventing triplex formation or when TFO was labeled with 32P instead of 125I. Mapping DSB sites with single base resolution showed that they are distributed within 10 bp of a maximum located exactly opposite the position of the [125I] IdC in the TFO. We estimate that on average the amount of DSB produced per decay is close to one.

Sequence specificity of (cyanomorpholino)adriamycin adducts in human cells

The highly reiterated alpha DNA tandem repeat was extracted from HeLa cells incubated with (cyanomorpholino)adriamycin (CMA) using mild techniques and subsequently probed for drug adducts by exonuclease III. The sequence specificity of the CMA-induced blockages was compared with that for blockages induced on the same DNA fragment when reacted in vitro. The sequence specificity of the drug-induced blockages was the same on both the isolated and the intact cell alpha DNA templates, with blockages predominantly associated with GpG sequences on either strand of the DNA.

Ultraviolet light-induced cleavage of DNA in the presence of iodoHoechst 33258: the sequence specificity of the reaction

IodoHoechst 33258 sensitizes DNA to cleavage by near ultraviolet light (UV-A). Following an earlier study which showed that the UV-induced cleavage is at discrete locations corresponding to the ligand binding sites, this paper reports a more extensive analysis of the sequence specificity of cleavage. The experiments involved use of double-stranded DNA synthesised on primed M13 templates. Analysis of cleavage in a 280bp sequence in M13mp18 and a 310bp sequence in three M13mp9 clones ('alpha-32', 'alpha-82' and 'alpha-22') derived from human alpha-DNA, showed that for all of the twenty-nine strong and very strong damage sites, cleavage was at the 3' end of a run of three or more consecutive AT base pairs. The extent of cleavage was higher for sites with consecutive Ts than for consecutive As, and greatest for the sequence cTTTTca. Comparison of three closely-related alpha-DNA clones enabled assessment of single bp changes and essentially confirmed the results of detailed analysis of binding cleavage sites in mp18 and alpha-32. Decreasing the input ratio of iodoHoechst/per bp DNA from 0.13 to 0.013 altered the sequence specificity, and sites possessing only three consecutive AT bps were generally not cleaved. The contributions of both the strength of ligand binding and the efficiency of photolytic cleavage to the overall extent of cleavage by UV/iodoHoechst are discussed, in view of the potential utility of the ligand as a probe of DNA conformation.

Interaction of Hoechst 33258 with a DNA triple helix

The interaction of Hoechst 33258 molecule, a minor groove binding drug, with T-A-T triple helix and A-T double helix was studied using circular dichroism spectroscopy and thermal denaturation. The triple helix consisted of an oligonucleotide (dA)12-x-(dT)12-x-(dT)12, where x is a hexa-ethylene glycol chain bridged between the 3' phosphate of one strand and the 5' phosphate of the following strand. This oligonucleotide is able to fold back on itself to form a very stable triplex. Circular dichroism spectroscopy demonstrates that Hoechst 33258 can bind to the triple helical structure. Spectral analysis shows that the bound drug exhibits a conformation and an environment slightly different in double-stranded and in triple-stranded structure. The affinity to the triple stranded structure is found smaller than to the double stranded one. Thermal denaturation experiments demonstrate that Hoechst 33258 destabilizes the triplex whereas it stabilizes the duplex.

Expression of histone and alkaline phosphatase genes in UMR 106-01 rat osteoblast-like cells exposed to the Hoechst dye H33342

The fluorescent Dye H33342 (H342) is a bis-benzimidazole used for intravital fluorescent staining. In this report, we found that H342 completely abolished histone 2a mRNA but had no effect on alkaline phosphatase gene expression and protein synthesis in UMR 106-01 rat osteoblast-like cells. The complete loss of histone 2a mRNA occurred after only 20 min of treatment with H342. This effect is unlikely to be a result of inhibition of DNA synthesis, which was only partly suppressed. The mechanism of the action of H342 on histone 2a mRNA is presently unknown.

Sequence-specific DNA damage using iodine-125-labeled antisense oligonucleotides

A procedure is described that cleaves single-stranded DNA with sequence specificity. This process involves attaching a DNA damaging agent to an oligonucleotide. This oligonucleotide delivers the DNA damaging agent, iodine-125, to a specific DNA sequence by complementary hybridization. 5-[125I]Iodo-2-deoxycytidine 5'-triphosphate was enzymatically incorporated into an oligonucleotide that was designed to hybridize to a single-stranded DNA target. 125I decays by electron capture and causes breaks in the target DNA. These breaks were observed on a DNA sequencing gel. After 22 days of exposure to the 125I-labeled oligonucleotide, significant damage was observed within 1 to 2 bases of the expected site of hybridization. Densitometry showed that after 48 days the amount of damage had approximately doubled. This method facilitates easy design and testing of oligonucleotides that could potentially be used to inactivate gene expression in a wide variety of organisms.

DNA ligands as radiomodifiers: studies with minor-groove binding bibenzimidazoles

An iodinated bibenzimidazole, iodoHoechst 33258, was previously reported to markedly sensitize DNA and cells to UV-A, exemplifying the potential of iodinated DNA ligands as radiosensitizers, a rational extension of sensitization by halogenated pyrimidines. However, unlike the latter sensitizers, iodoHoechst 33258 is not a sensitizer of ionizing radiation, presumably due to the innate radioprotective properties of the uniodinated ligand. Experiments with purified DNA show that both Hoechst 33258 and Hoechst 33342 decrease the yield the radiation-induced DNA strand breakage. The ligands bind at discrete sites in the minor groove of DNA, and analysis on DNA sequencing gels show pronounced protection at the ligand binding sites, as well as more generalized protection. The extent of protection of strand breakage on plasmid DNA and the fact that it persists in the presence of 0.5 M NaCl (which prevents low affinity ionic binding between the high affinity sites) suggests that the protective effects of bound ligand are not confined to the high affinity binding sites in the minor groove. The mechanisms of this generalized protection is unknown, but there is some evidence indicating that the H-atom donation from the ligand may account for the site-specific protection. The extent of protection is much diminished, but still evident, in the presence of 100 mM mannitol, a known hydroxyl radical scavenger, indicating that some of the protective effects might relate to DNA damage mediated by direct action. Further evaluation of the mechanisms of protection should enable development of both more active radioprotectors and, by elimination of the radioprotective features from halogenated DNA ligands, more effective radiosensitizers.

Sequence-specific interaction of Hoechst 33258 with the minor groove of an adenine-tract DNA duplex studied in solution by 1H NMR spectroscopy

The interaction of Hoechst 33258 with the minor groove of the adenine-tract DNA duplex d(CTTTTGCAAAAG)2 has been studied in both D2O and H2O solutions by 1D and 2D 1H NMR spectroscopy. Thirty-one nuclear Overhauser effects between drug and nucleotide protons within the minor groove of the duplex, together with ring-current induced perturbations to the chemical shifts of basepair and deoxyribose protons, define the position and orientation of the bound dye molecules. Two drug molecules bind cooperatively and in symmetry related orientations at the centre of the 5'-TTTT and 5'-AAAA sequences with the binding interactions spanning only the four A-T basepairs. The positively charged N-methylpiperazine moieties point towards the centre of the duplex while the phenol groups are disposed towards the 3'-ends of the sequence. Resonance averaging is apparent for both the D2/D6 and D3/D5 phenol protons and D2"'/D6"' and D3"'/D5"' of the N-methylpiperazine ring and is consistent with these groups being involved in rapid rotation or ring-flipping motions in the bound state. Interstrand NOEs between adenine H2s and deoxyribose H1' are consistent with a high degree of propeller twisting of the A-T basepairs at the binding site of the aromatic benzimidazole and phenol rings of Hoechst. The data imply that the minor groove is particularly narrow with many contacts between the complementary curved surfaces of the drug and DNA indicating that strong van der Waals interactions, involving the floor and the walls of the minor groove, stabilize the complex. In our model the NH groups of the benzimidazole rings are positioned to make a pair of bifurcated hydrogen bonds with the adenine N3 and thymine O2 on the floor of the minor groove.

Radiation sensitization by an iodine-labelled DNA ligand

An iodinated DNA ligand, iodo Hoechst 33258, which binds in the minor groove of DNA, enhances DNA strand breakage and cell killing by UV-A irradiation. The sites of UV-induced strand breaks reflect the known sequence specificity of the ligand.

Differentiation of EC cells in vitro by the fluorescent dye Hoechst 33342

The fluorescent dye Hoechst 33342 is able to differentiate F9 EC cells at low concentrations. This differentiation is accompanied by synthesis of large amounts of laminin, production of a well-developed cytoskeleton, disappearance of the SSEA-1 antigen, and synthesis of large amounts of fibronectin, all characteristics of the primitive endoderm. The dye immediately blocks the cells at the S/G2 phase of the cell cycle and produces a complete arrest in proliferation. This effect is not specific for the nullipotent F9 cell line, as multipotent EC cell lines like PCC3, P19, and PCC4 can also be easily differentiated into the same pathway by treatment with the Hoechst dye. In contrast, the dye has no remarkable effects on terminal differentiated, immortalized cells like NIH 3T3 or the parietal endoderm-like cell PYS-2.

Binding of a Hoechst dye to d(CGCGATATCGCG) and its influence on the conformation of the DNA fragment

Hoechst dye 33258 is a planar drug molecule that binds to the minor groove of DNA, especially where there are a number of A.T base pairs. We have solved the structure of the Hoechst dye bound to the DNA dodecamer d(CGCGATATCGCG) at 2.3 A. This structure is compared to that of the same dodecamer with the minor-groove-binding drug netropsin bound to it, as well as to structures that have been solved for this Hoechst dye bound to a DNA dodecamer containing the central four base pairs with the sequence AATT. We find that the position of the Hoechst drug in this dodecamer is quite different from that found in the other dodecamer since it has an opposite orientation compared to the other two structures. The drug covers three of the four A.T base pairs and extends its piperazine ring to the first G.C base pair adjacent to the alternating AT segment. Furthermore, the drug binding has modified the structure of the DNA dodecamer. Other DNA dodecamers with alternating AT sequences show an alternation in the size of the helical twist between the ApT step (small twist) and the TpA step (large twist). In this structure the alternation is reversed with larger twists in the ApT steps than in the TpA step. In addition, there is a rotation of one of the thymine bases in the DNA dodecamer that is associated with hydrogen bonding to the Hoechst drug. This structure illustrates the considerable plasticity found in the DNA molecule when it binds to different planar molecules inserted into the minor groove.

Sequence specificity of 125I-labelled Hoechst 33258 damage in six closely related DNA sequences

The sequence selectivity of [125I]Hoechst 33258 in six 340 base-pair DNA sequences has been investigated. [125I]Hoechst 33258, which is a bis-benzimidazole and binds to the minor groove of B-DNA, preferentially binds to A + T-rich regions of DNA. Six out of nine strong binding sites contained four or more consecutive A.T base-pairs, while the other three strong binding sites were AAGGATT, TATAGAAA (the peak of damage was in the run of 3 A residues) and AAA. One of the six weak binding sites had five consecutive A.T base-pairs, two of the weak binding sites had three, and three did not have any. In addition to genomic 340 base-pair alpha RI-DNA (which is a tandem repeat in human cells), five 340 base-pair alpha RI-DNA clones were generated that differed from the genomic "consensus" sequence by a number of random base alterations. The effect of these base changes on the sequence specificity of [125I]Hoechst 33258 damage indicated that of the base changes that interrupted 14 binding sites, six decreased and eight did not change the extent of damage, while two sites changed position. Of the base alterations that augmented 17 binding sites, five increased, two decreased and ten did not alter the degree of cleavage, while ten sites changed position. It was concluded from the data that, while runs of consecutive A.T base-pairs was the most important parameter that determines [125I]Hoechst 33258 binding, other factors including position in the DNA sequence, nearest neighbour and long-range interactions were also important.